RetrogeneDB ID: retro_mmul_1007

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 13:109601604..109602051(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: SRSF3
• Ensembl ID: ENSMMUG00000014306
• Aliases: None
• Description: None

Sequence

>retro_mmul_1007
GTTTATGCAGGCAATCTTGGAAACAATGGCAACAAGACTGAATTGGAACGGGCTTTCGGCTACTATAGACCACTCTGAAG
TGTGTGGGTTGCTAGAAATCCTCCCGGCTTTACTTTTGTTGAATTTGAAGATCCCCGAGGTGCAGCTGATGCGATCCGAG
AGCTAGATGGAAGAACACCATATGGTCGCTGTGTAGGAGTGGAACTGTCGAATGGTGAAAAAAGAAGTAGAAATCGTGGC
CCACCTCCCTCTCGGGGTCGTCGCCCTCAAGATGATTATCGCAGGAGGCGTCCTCCACCTCGTCGCAGATCTCCAAGGAG
AAGCCTCTCTCGCTGCGGGAGCAGGTCCCTTTCTAGAGTTAGGAGAAGAGAGAGATCGCTGTCTCCGGAGAGAAATCACA
AGCCATGATCCTTCTCTAGGTTTCGTAGGCCATCTAGGTCAAATGAG

Alignment

ORF - retro_mmul_1007 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.44 %
• Parental protein coverage: 92.07 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELS
          VY.GNLGNNGNKTELERAFGYY.PL.SVWVARNPPGF.FVEFEDPR.AADA.RELDGRT..G..V.VELS
Retrocopy VYAGNLGNNGNKTELERAFGYYRPL*SVWVARNPPGFTFVEFEDPRGAADAIRELDGRTPYGRCVGVELS

Parental  NGEKRSRNRGPPPSWGRRPRDDYRRRSPPPRRRSPRRRSFSRSRSRSLSRDRRRERSLSRERNHKPSRSF
          NGEKRSRNRGPPPS.GRRP.DDYRRR.PPPRRRSP.RRS.SR..SRSLSR.RRRERSLS.ERNHKP..SF
Retrocopy NGEKRSRNRGPPPSRGRRPQDDYRRRRPPPRRRSP-RRSLSRCGSRSLSRVRRRERSLSPERNHKP-*SF

Parental  SRSRSRSRSNE
          SR.R..SRSNE
Retrocopy SRFRRPSRSNE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	75.63 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	61.00 RPM
SRP007412_cerebellum	0.00 RPM	107.84 RPM
SRP007412_heart	0.06 RPM	91.04 RPM
SRP007412_kidney	0.23 RPM	86.50 RPM
SRP007412_liver	0.08 RPM	51.10 RPM
SRP007412_testis	0.04 RPM	140.14 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1007 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1007 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1007 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2140

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016062	5 retrocopies	retro_cjac_1035, retro_cjac_1969, retro_cjac_2006, retro_cjac_620, retro_cjac_746,
Echinops telfairi	ENSETEG00000010117	2 retrocopies	retro_etel_2064, retro_etel_445,
Loxodonta africana	ENSLAFG00000018193	2 retrocopies	retro_lafr_1219, retro_lafr_80,
Myotis lucifugus	ENSMLUG00000010671	6 retrocopies	retro_mluc_1205, retro_mluc_1312, retro_mluc_1554, retro_mluc_2283, retro_mluc_278, retro_mluc_51,
Macaca mulatta	ENSMMUG00000014306	4 retrocopies	retro_mmul_1007 , retro_mmul_1042, retro_mmul_1642, retro_mmul_2359,
Macaca mulatta	ENSMMUG00000016494	1 retrocopy	retro_mmul_2154,
Mus musculus	ENSMUSG00000071172	9 retrocopies	retro_mmus_100, retro_mmus_1347, retro_mmus_1749, retro_mmus_2294, retro_mmus_2337, retro_mmus_2433, retro_mmus_2654, retro_mmus_2933, retro_mmus_3629,
Otolemur garnettii	ENSOGAG00000000502	6 retrocopies	retro_ogar_1850, retro_ogar_1959, retro_ogar_2131, retro_ogar_2783, retro_ogar_597, retro_ogar_803,
Sus scrofa	ENSSSCG00000001564	1 retrocopy	retro_sscr_1038,
Ictidomys tridecemlineatus	ENSSTOG00000014280	5 retrocopies	retro_itri_123, retro_itri_502, retro_itri_664, retro_itri_857, retro_itri_901,